Cyclin-dependent kinases (Cdks) require activating T-loop phosphorylation, a modification considered constitutive. Here, we examine the regulation of the Cdk-activating kinase, Cak1, in budding yeast. We measure Cak1 levels and the activating T169 phosphorylation of Cdc28 (the budding yeast Cdk) in different nutrients. The abundance of Cak1 and T169 phosphorylation is reduced in cells that proliferate very slowly or enter quiescence. A small upstream open reading frame (uORF) in CAK1 represses Cak1 synthesis, especially in poor growth conditions. Eliminating the uORF increases Cak1 levels but does not alter proliferation kinetics under most laboratory contexts. Instead, it reduces the viability of quiescent cells. In cells lacking several type 2 C protein phosphatases, which remove the T169 phosphorylation, initiation of cell division is accelerated in the absence of the uORF in CAK1. Our results suggest an unexpected layer of control, impinging on the activating phosphorylation of the Cdk. The uORF-mediated repression of Cak1 synthesis directly couples protein synthesis to the activity of the core cell cycle machinery. Levels of the Cdk-activating kinase Cak1 and the active Cdk Cdc28 are reduced in yeast in poor growth conditions, because Cak1 translation is repressed by an uORF, coupling the cell’s protein-synthesis capacity to the activation of master regulators of division. Levels of the Cdk-activating kinase Cak1 and the active Cdk Cdc28 are reduced in yeast in poor growth conditions, because Cak1 translation is repressed by an uORF, coupling the cell’s protein-synthesis capacity to the activation of master regulators of division.
Vimentin intermediate filaments are a hallmark of aggressive tumours and are widely linked to invasion and EMT, yet how vimentin-dependent mechanics shape genome maintenance and therapy response is unclear. Here we show that vimentin, particularly under compressive load, promotes DNA repair competence. In contrast, vimentin-negative cells show impaired DNA damage sensing and downstream signaling, ultimately leading to decreased apoptosis and promoting cell survival under genotoxic stress at the expense of genomic stability. Using controlled cell compression together with genetic and pharmacological perturbations, we find that loss of vimentin in glioblastoma cells limits the expression and activity of core repair pathways because of induced nuclear mechanical compression. Relieving nuclear compression restores DNA damage accumulation and repair kinetics. Functionally, suppression of DNA damage responses enhances survival after clinically relevant DNA-damaging treatments, including temozolomide, X-Ray radiation and cell invasion through tight spaces. These findings invert the prevailing view that vimentin’s contribution to tumour progression stems from enhanced migration and identify a mechanochemical vimentin-nucleus axis that tunes DNA damage responses to favor therapy tolerance and genome evolution. We show that vimentin mechanically protects the nucleus from compressive forces, thereby maintaining chromatin organization and DNA damage response (DDR) pathways. Loss of vimentin or increased mechanical compression suppresses DDR signaling, enhances survival after genotoxic stress, and may promote therapy resistance and genomic instability, revealing an unexpected mechanochemical role for vimentin in cancer progression. We show that vimentin mechanically protects the nucleus from compressive forces, thereby maintaining chromatin organization and DNA damage response (DDR) pathways. Loss of vimentin or increased mechanical compression suppresses DDR signaling, enhances survival after genotoxic stress, and may promote therapy resistance and genomic instability, revealing an unexpected mechanochemical role for vimentin in cancer progression.
Maternal obesity increases the risk of abnormal cardiac development during gestation. However, the underlying metabolic determinants contributing to these defects remain insufficiently understood. In this study, reduced butyrate is identified in HFD-fed mice and their embryos, accompanied by fetal cardiac abnormalities, including ventricular wall thickening, sarcomere elongation, and myofibril disorganization. These abnormalities can be rescued by butyrate supplementation. For in vitro verification in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and organoids, butyrate effectively restores palmitate-induced contractile dysfunction and myofibrillar disarray. Mechanistically, drug affinity-responsive target stability (DARTS) assays and molecular docking analyses identify pleckstrin homology and RhoGEF domain containing G3 (PLEKHG3), which enables actin binding activity, as a direct target of butyrate. Butyrate binding enhances the interaction between PLEKHG3 and F-Actin, thereby promoting contractility and orderly assembly of myofibrils. Conversely, loss-of-function mutation (Q175A) in PLEKHG3 disrupts PLEKHG3/F-Actin binding and abrogates protective effects of butyrate. Collectively, these findings reveal that butyrate ameliorates obesity-induced embryonic cardiac defects by modulating the PLEKHG3/F-Actin axis, highlighting its potential as a therapeutic metabolite for mitigating cardiac abnormalities associated with maternal obesity. Reduced butyrate emerges as a hallmark of dysregulated short-chain fatty acid metabolism in the context of maternal obesity, and butyrate supplementation could ameliorate embryonic cardiac defects by modulating the PLEKHG3/F-Actin axis. These findings highlight butyrate as a promising therapeutic strategy to mitigate the intergenerational impacts of maternal obesity on fetal cardiac development. Reduced butyrate emerges as a hallmark of dysregulated short-chain fatty acid metabolism in the context of maternal obesity, and butyrate supplementation could ameliorate embryonic cardiac defects by modulating the PLEKHG3/F-Actin axis. These findings highlight butyrate as a promising therapeutic strategy to mitigate the intergenerational impacts of maternal obesity on fetal cardiac development.
Proopiomelanocortin (POMC) neurons in the arcuate nucleus of the hypothalamus (ARC) play a critical role in energy homeostasis. 5’-adenosine monophosphate-activated protein kinase (AMPK) is a serine/threonine kinase, which acts as the main energy sensor in the cell. The heterotrimeric AMPK results from the combination of a catalytic α subunit (α1, α2) with two regulatory subunits, β (β1, β2) and γ (γ1, γ2 and γ3). Hypothalamic AMPK plays a key role in the control of energy balance, but current evidence shows that the precise combination of its heterotrimeric components determines its physiological action. Our findings show that AMPKα1 ablation in POMC neurons has a sex-dependent protective effect against diet-induced obesity because of increased thermogenesis in brown adipose tissue (BAT) in males, but not in females. At the molecular level, deletion of AMPKα1 in POMC neurons disrupts the ARC phosphoproteome and is associated with ameliorated endoplasmic reticulum (ER) stress and reduced ceramide content. These findings highlight the complex function of the different AMPK subunits in the hypothalamic regulation of energy balance. Deletion of AMPK1 in POMC neurons protects male mice against diet-induced obesity by increasing brown adipose tissue thermogenesis and energy expenditure, without affecting food intake. This effect is associated with reduced hypothalamic ER stress and ceramide content, highlighting a sex-specific and subunit-specific role of hypothalamic AMPK in energy balance. Deletion of AMPK1 in POMC neurons protects male mice against diet-induced obesity by increasing brown adipose tissue thermogenesis and energy expenditure, without affecting food intake. This effect is associated with reduced hypothalamic ER stress and ceramide content, highlighting a sex-specific and subunit-specific role of hypothalamic AMPK in energy balance.
Gene activation and repression is an integral part of embryonic development and tissue formation. Changes in chromatin organisation dictate accessibility to gene regulatory elements, controlling gene expression. Although several molecular regulators of lymphatic endothelial cell (LEC) development have been identified, the role of chromatin organisation in the acquisition of LEC identity remains unclear. In this study, we combine HiC and ATAC-sequencing to map 3D chromatin architecture and accessibility in LECs and blood endothelial cells (BECs). We identify cell type-specific topologically associating domains (TADs), and discovered TAD boundaries changes and differentially segregating enhancers in lymphatic-associated loci, such as prox1a and tbx1. Our multi-omic approach also defines the regulatory logic of nine LEC-enriched genes. In vivo validation of ATAC- and HiC-based enhancers confirms their activity in LECs. Leveraging these datasets, we reconstructed mafba tissue-specific regulatory networks identifying a genetic interaction with tfe3a in vivo limiting ectopic vessel formation. Overall, our work provides a powerful resource of multi-omic datasets that can be used to systematically determine the regulatory networks governing LEC identity and genes linked to lymphatic disease. The topologically associating domains (TADs) and chromatin accessibility of lymphatic endothelial cells diverge from those of blood endothelial cells. These differences underlie the activation of LEC-specific regulatory networks governing cell identity and involving genes linked to lymphatic disease. The topologically associating domains (TADs) and chromatin accessibility of lymphatic endothelial cells diverge from those of blood endothelial cells. These differences underlie the activation of LEC-specific regulatory networks governing cell identity and involving genes linked to lymphatic disease.
Impaired energy production is a hallmark of mitochondrial oxidative phosphorylation (OXPHOS) defects. However, secondary metabolic disturbances also represent an important trigger for pathologies originating from OXPHOS aberrations. Here we show that cells with OXPHOS deficiencies accumulate triacylglycerols enriched in polyunsaturated fatty acids (PUFAs), which are stored in lipid droplets. Sequestration of PUFAs is a critical component of a broader stress response, which also includes downregulation of cellular desaturases and upregulation of glutathione peroxidase 4 (GPX4). We demonstrate that this mechanism represents a physiologically relevant protective strategy, manifesting in cells under hypoxia and in immortalised fibroblasts derived from patients with primary mitochondrial complex IV deficiency. As a proof of principle, we observe elevated PUFA-enriched triacylglycerols in the plasma of patients with Myoclonic Epilepsy with Ragged Red Fibres (MERRF). Our findings reveal a novel protective mechanism against ferroptosis, which preserves membrane integrity when mitochondrial respiration is compromised. OXPHOS-deficient cells activate a coordinated multilayered polyunsaturated fatty acid (PUFA) stress response, which preserves membrane integrity against lipid peroxidation-driven ferroptosis. It is conserved across distinct OXPHOS complex deficiencies, is recapitulated under hypoxia, and is detectable in patients with mitochondrial disease. OXPHOS-deficient cells activate a coordinated multilayered polyunsaturated fatty acid (PUFA) stress response, which preserves membrane integrity against lipid peroxidation-driven ferroptosis. It is conserved across distinct OXPHOS complex deficiencies, is recapitulated under hypoxia, and is detectable in patients with mitochondrial disease.
Scientific knowledge is advancing faster than ever, yet its authority is increasingly detached from the way information circulates in public debates. This article proposes a transparent, professionally curated repository of validated scientific and educational materials as shared infrastructure for science communication.
Using game theory, we demonstrate how performance metrics in academic science function as a non-monetary currency that solves the principal-agent problem in science and extracts high efforts from researchers. In light of increasingly scarce resources, these incentives require structural redesign of their mechanism to prevent strategic manipulation.
This article discusses speculative design as a creative practice that uses imagined socio-technological scenarios to provoke debate and reflection in the context of reproductive technologies.
Cancer cells frequently show elevated glucose consumption to support proliferation and survival. This led to the assumption that glycolytic inhibitors could be effective in cancer treatment. However, barriers to clinical implementation remain. Adaptive strategies, such as metabolizing alternative nutrients, may play a role. Here, we investigated the use of an understudied sugar, mannose, in lung cancer cells and xenografts. Stable isotope tracing reveals enhanced contribution of mannose to GDP-mannose and GDP-fucose, key glycosylation precursors, upon treatment with the glycolytic inhibitor 2-deoxyglucose (2-DG) or glucose starvation in vitro. Mannose restores the glucose-withdrawal-induced decrease of GDP-mannose and GDP-fucose pools, and partially rescues proliferation upon 2-DG treatment or glucose deprivation. 13C6-mannose infusion in patient-derived xenograft mice reveals a considerable contribution of mannose to GDP-mannose and GDP-fucose in tumors, which is further enhanced by 2-DG. In normal lungs, the pathway is only partially active. Mannose is also shuttled towards glycolysis in lung tumors in vivo and glucose-deprived cells in vitro. In conclusion, mannose utilization for glycosylation precursor synthesis represents an adaptive strategy in lung cancer cells under metabolic stress. Alternative nutrients might limit the efficacy of glycolytic intervention in cancer treatment. This study highlights the importance of mannose utilization for glycosylation precursors upon inhibition of glycolysis or glucose starvation. Alternative nutrients might limit the efficacy of glycolytic intervention in cancer treatment. This study highlights the importance of mannose utilization for glycosylation precursors upon inhibition of glycolysis or glucose starvation.
piRNAs are small regulatory RNAs with critical roles in transposon silencing and regulation of gametogenesis. Phase separation is a driving force for piRNA biogenesis machinery formation; however, the specific piRNA-related proteins that mediate phase separation and how they coordinate to drive piRNA production remain incompletely understood. Through systematic screening, we show here that TDRD5 undergoes phase separation to promote piRNA biogenesis. TDRD5 condensation is mediated by its Lotus domains and an intrinsically disordered region enriched with aromatic residues. Furthermore, TDRD1 and TDRD5 colocalize and synergistically enhance each other’s phase separation. TDRD5 phase separation is required for intermitochondrial cement assembly and fetal piRNA processing in fetal/neonatal gonocytes but is dispensable for pachytene piRNA biogenesis in adult mice. TDRD5 phase separation deficiency impairs male fertility in mice and may contribute to human male infertility. Our findings highlight the critical but diverse contributions of phase-separated proteins to germ granule assembly and piRNA production. TDRD5 undergoes phase separation to promote intermitochondrial cement assembly and piRNA biogenesis, which is important for transposon silencing and male fertility in mice. TDRD5 undergoes phase separation to promote intermitochondrial cement assembly and piRNA biogenesis, which is important for transposon silencing and male fertility in mice.
Olfactory dysfunction is a major symptom of COVID-19 syndrome. The critical genes contributing to SARS-CoV-2 infection are not fully understood. Here, we identified Cadherin 1 (CDH1), a hub in the interaction network of viral entry-related genes in human and mouse olfactory epithelium (OE), is coexpressed with ACE2 in sustentacular cells. CDH1 overexpression attenuates pseudoviral and authentic SARS-CoV-2 infection in ACE2-expressing HEK293T cells and human OE organoids, whereas CDH1 downregulation promotes infection. Mechanistically, CDH1 interacts with ACE2 and competes with the Spike protein for ACE2 binding. Three residues in CDH1 (W59, N168, and Q197) are critical for CDH1-ACE2 binding, and mutations at these residues weaken the interaction and enhance pseudoviral infection. In the OE of deceased COVID-19 patients, cells with higher viral load exhibit lower CDH1 expression. This inverse correlation between CDH1 expression and SARS-CoV-2 load is validated in human bronchial epithelial cells, and in lung ciliated and secretory cells. Collectively, our findings establish CDH1 as a novel restriction factor for SARS-CoV-2 infection in the olfactory system, potentially offering a target for antiviral therapy. In this study, we identify CDH1 as a critical and novel restriction factor for SARS-CoV-2 infection in the olfactory system. This may offer an ideal target for antiviral therapy. In this study, we identify CDH1 as a critical and novel restriction factor for SARS-CoV-2 infection in the olfactory system. This may offer an ideal target for antiviral therapy.
After fertilization, maternally deposited mRNAs are cleared, and de novo transcription is initiated through zygotic genome activation (ZGA), a core event of the maternal-to-zygotic transition in mice. 2-cell-like cells (2CLCs), a rare MERVL-positive subpopulation of mouse embryonic stem cells, partially recapitulate transcriptional features of 2-cell embryos. Although canonical MERVL-high 2CLCs depend on DUX, Dux knockout embryos can develop to term, suggesting that 2CLC models do not fully capture DUX-independent pathways associated with preimplantation transcriptional programs. Here, we show that disruption of C-terminal binding protein 1/2 (Ctbp1/2) activates both DUX-dependent minor ZGA-associated genes and DUX-independent major ZGA- and post-ZGA-associated programs. Pramel7 is derepressed independently of DUX and contributes to subsets of both programs. PRAMEL7 overexpression partially rescues transcriptional defects caused by Dux deletion and is associated with UHRF1 downregulation and DNA demethylation-linked activation of post-ZGA-associated genes. These findings identify CtBP1/2 as repressors of multiple early embryonic transcriptional programs in mouse embryonic stem cells. CtBP1/2 loss activates both DUX-dependent minor-ZGA and DUX-independent major/post-ZGA transcriptional programs in mouse ESCs. PRAMEL7 links these pathways by promoting Dux expression and UHRF1 downregulation-associated DNA demethylation. CtBP1/2 loss activates both DUX-dependent minor-ZGA and DUX-independent major/post-ZGA transcriptional programs in mouse ESCs. PRAMEL7 links these pathways by promoting Dux expression and UHRF1 downregulation-associated DNA demethylation.
The soil microbiome plays a crucial role for crop yield and plant nutrient content, and for sequestering carbon dioxide from the atmosphere. Recent advances in soil engineering therefore have great potential for sustainable and regenerative agriculture while contributing to climate resilience.
Multi-criteria sustainability analyses, based on life cycle thinking and assessment, are critical to help us navigate sustainable transitions in food and agriculture. This includes current industrial agriculture as well as new technologies such as vertical farming, cellular agriculture and macronutrient synthesis that may well transform the future of food.
Affecting 110 million African children, schistosomiasis control demands an urgent shift from drug treatments to permanent transmission interruption. This requires pairing paediatric drug formulations and new interventions including any new vaccines with locally-relevant multisectoral policy, WASH infrastructure and community-led behaviour change as well as sustained domestic financing.
